1J54 - JenaLib

Title :   STRUCTURE OF THE N-TERMINAL EXONUCLEASE DOMAIN OF THE EPSILON SUBUNIT OF E.COLI DNA POLYMERASE III AT PH 5.8

Authors :   S. Hamdan, P. D. Carr, S. E. Brown, D. L. Ollis, N. E. Dixon

Date :   22 Jan 02 (Deposition) - 16 Oct 02 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.70

Chains :   Asym./Biol. Unit : A

Keywords :   Dna Polymerase Proofreading Domain, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Hamdan, P. D. Carr, S. E. Brown, D. L. Ollis, N. E. Dixon
Structural Basis For Proofreading During Replication Of The Escherichia Coli Chromosome
Structure V. 10 535 2002
PubMed-ID: 11937058 | Reference-DOI: 10.1016/S0969-2126(02)00738-4
(for further references see the PDB file header)

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 6)

Sites (6, 6)

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:12 , GLU A:14 , ASP A:167 , TMP A:2000	BINDING SITE FOR RESIDUE MN A 3000
2	AC2	SOFTWARE	ASP A:12 , TMP A:2000 , HOH A:6001 , HOH A:6002 , HOH A:6003 , HOH A:6004	BINDING SITE FOR RESIDUE MN A 3001
3	AC3	SOFTWARE	ASP A:12 , THR A:13 , GLU A:14 , THR A:15 , MET A:18 , GLU A:61 , VAL A:65 , HIS A:66 , PHE A:102 , HIS A:162 , ASP A:167 , MN A:3000 , MN A:3001 , EDO A:6000 , HOH A:6001 , HOH A:6003 , HOH A:6004 , HOH A:6035 , HOH A:6145 , HOH A:6170	BINDING SITE FOR RESIDUE TMP A 2000
4	AC4	SOFTWARE	THR A:123	BINDING SITE FOR RESIDUE EDO A 4000
5	AC5	SOFTWARE	ARG A:7	BINDING SITE FOR RESIDUE EDO A 5000
6	AC6	SOFTWARE	MET A:18 , PHE A:102 , TMP A:2000	BINDING SITE FOR RESIDUE EDO A 6000

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Asymmetric/Biological Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
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Chain A from PDB  Type:PROTEIN  Length:174
 aligned with DPO3E_ECOLI | P03007 from UniProtKB/Swiss-Prot  Length:243

    Alignment length:174
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176    
          DPO3E_ECOLI     7 RQIVLDTETTGMNQIGAHYEGHKIIEIGAVEVVNRRLTGNNFHVYLKPDRLVDPEAFGVHGIADEFLLDKPTFAEVADEFMDYIRGAELVIHNAAFDIGFMDYEFSLLKRDIPKTNTFCKVTDSLAVARKMFPGKRNSLDALCARYEIDNSKRTLHGALLDAQILAEVYLAMTG 180
               SCOP domains d1j54a_ A: N-terminal exonuclease domain of the epsilon subunit of DNA polymerase III                                                                                          SCOP domains
               CATH domains 1j54A00 A:7-180  [code=3.30.420.10, no name defined]                                                                                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeee..............eeeeeeeeee..ee....eeee.......hhhhhhhhh.hhhhhh...hhhhhhhhhhhhhh..eeee..hhhhhhhhhhhhhhh.....hhhhh.eeeehhhhhhhhh.....hhhhhhhhh..........hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1j54 A   7 RQIVLDTETTGMNQIGAHYEGHKIIEIGAVEVVNRRLTGNNFHVYLKPDRLVDPEAFGVHGIADEFLLDKPTFAEVADEFMDYIRGAELVIHNAAFDIGFMDYEFSLLKRDIPKTNTFCKVTDSLAVARKMFPGKRNSLDALCARYEIDNSKRTLHGALLDAQILAEVYLAMTG 180
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
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	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (1, 1)

Pfam Domains (0, 0)

Gene Ontology (15, 15)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (DPO3E_ECOLI | P03007)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0003887	DNA-directed DNA polymerase activity	Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1); the synthesis of DNA from deoxyribonucleotide triphosphates in the presence of a DNA template and a 3'hydroxyl group.
	GO:0004527	exonuclease activity	Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' or 5' end.
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0004518	nuclease activity	Catalysis of the hydrolysis of ester linkages within nucleic acids.
	GO:0003676	nucleic acid binding	Interacting selectively and non-covalently with any nucleic acid.
	GO:0016779	nucleotidyltransferase activity	Catalysis of the transfer of a nucleotidyl group to a reactant.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0016740	transferase activity	Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
	GO:0071897	DNA biosynthetic process	The cellular DNA metabolic process resulting in the formation of DNA, deoxyribonucleic acid, one of the two main types of nucleic acid, consisting of a long unbranched macromolecule formed from one or two strands of linked deoxyribonucleotides, the 3'-phosphate group of each constituent deoxyribonucleotide being joined in 3',5'-phosphodiester linkage to the 5'-hydroxyl group of the deoxyribose moiety of the next one.
	GO:0006260	DNA replication	The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA.
	GO:0045004	DNA replication proofreading	Correction of replication errors by DNA polymerase using a 3'-5' exonuclease activity.
	GO:0090305	nucleic acid phosphodiester bond hydrolysis	The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
cellular component
	GO:0044776	DNA polymerase III, core complex	The DNA polymerase III core complex consists of the alpha,epsilon and theta subunits and is carries out the polymerase and the 3'-5' exonuclease proofreading activities.

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